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<font size="+3"><b>SH-SY5Y Sequencing Project</b></font>
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    <li><a href="#summary"><SPAN TITLE="Project summary and downloads">Summary Downloads</SPAN></a></li>
    <li><a href="#SNP"><SPAN TITLE="Explore single nucleotide polymorphisms and short insertion/deletion mutations. Detail links are provided to 1000 Genomes and dbSNP">SNP Indel</SPAN></a></li>
    <li><a href="#CNV">Copy Number</a></li>
    <li><a href="#STV"><SPAN TITLE="Displays recorded structural variations with frequency and sequence details, An upper case letter in a DNA consensus sequence indicates that the nucleotide is preserved in that position in all sequences used to make the consensus. A lower case letter is the most common nucleotide in a variable position.">Structural Variation</SPAN></a></li>
    <li><a href="#RNASeq">RNASeq</a></li>
    <li><a href="#Geo"><SPAN TITLE="Contains collections of SH-SY5Y GEO experiments organized with its expressed genes">GEO Microarray</SPAN></a></li>
    <li><a href="#Protein">Proteomics</a></li>
    <li><a href="#Metabolite">Metabolomics</a></li>
    <li><a href="#Sequencing"><SPAN TITLE="Find variant sequence on SH-SY5Y genes">Sequence</SPAN></a></li>
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  <div id="summary">
   <div>The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative disease. 
     We have used a systems genomics approach to characterize the SH-SY5Y cell line using whole-genome sequencing to determine the genetic background of the cell line and use transcriptomics, proteomics and metabolomics data together with a network analysis approach to evaluate the suitability of the SH-SY5Y cell line as a model system to study Parkinson's disease. <a href="#" onclick="manudialog();"><font color="blue">Manuscript</font></a><br><br>
     <table><tr><td><a href="images/figure1.png" target="_blank"><img class='prev' src="images/figure1_p.png" alt="circos"></a></td> 
	 <td><a href="images/figure2.png" target="_blank"><img class='prev' src="images/figure2_p.png" alt="chromosomes"></a></td></tr><tr> <td>Figure 1: Circos plot of the SH-SY5Y genome. Tracks represent (from outside to inside) karyotype for each chromosome, copy number variation (red > 2, green = 2, black < 2), density of small variants (bin size = 1Mb), homozygous small variant percentage (bin size = 1 Mb). Arcs represent chromosomal breakpoints (red = rare breakpoints not found in Complete Genomics Baseline dataset).
   </td><td>Figure 2: Copy number variation events detected by CG (left half of chromosomes) and microarray analysis(right half).
Regions are highlighted for copy number gain (red) and loss (blue). The major events partial trisomy of chromosome 1 and 2, complete trisomy of chromosome 7, gain in 17q and loss in 22q were confirmed.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;                                                                                                                                                  </td></tr></table>
   <br><font color="blue">Download Omics results</font>
   <br><ul>
     <li><a href="data/raw/SNP.gz">SNP (gz)</a></li>
     <li><a href="data/raw/CNV.tsv">CNV</a></li>
     <li><a href="data/raw/STV.tsv">STV</a></li>
     <li><a href="data/raw/RNASeq.gz">RNASeq (gz)</a></li>
     <li><a href="data/raw/microarray_gse9169.gz">Microarray GSE9169 (gz)</a>&nbsp;<a href="data/raw/microarray_shsy5y.gz">SH-SY5Y (gz)</a></li>
     <li><a href="data/raw/Protein.tsv">Protein</a></li>
     <li><a href="data/raw/Metabolomics.tsv">Metabolomics</a></li>
     <li><a href="data/raw/shsy5y.short_variants.fa.gz">Fasta (gz)</a>&nbsp;<a href="data/raw/shsy5y.short_variants.fa.fai">index</a></li>
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